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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-03-04, 09:26 EST based on data in: /local/workdir/zx54/Ziyu_amplicon_project/analysis/00_FastQC/fastqc_reports


        General Statistics

        Showing 372/372 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        SRR13675761_1
        94.5%
        54%
        0.1
        SRR13675761_2
        92.3%
        53%
        0.1
        SRR13675762_1
        92.7%
        55%
        0.1
        SRR13675762_2
        89.7%
        54%
        0.1
        SRR13675763_1
        93.7%
        53%
        0.1
        SRR13675763_2
        93.2%
        52%
        0.1
        SRR13675764_1
        90.9%
        51%
        0.1
        SRR13675764_2
        92.4%
        52%
        0.1
        SRR13675765_1
        94.0%
        55%
        0.1
        SRR13675765_2
        92.4%
        55%
        0.1
        SRR13675766_1
        95.1%
        55%
        0.0
        SRR13675766_2
        94.3%
        54%
        0.0
        SRR13675767_1
        92.5%
        52%
        0.1
        SRR13675767_2
        91.8%
        51%
        0.1
        SRR13675768_1
        91.9%
        56%
        0.1
        SRR13675768_2
        92.0%
        55%
        0.1
        SRR13675769_1
        91.5%
        53%
        0.1
        SRR13675769_2
        90.9%
        52%
        0.1
        SRR13675770_1
        91.8%
        52%
        0.1
        SRR13675770_2
        90.8%
        52%
        0.1
        SRR13675771_1
        97.3%
        53%
        0.1
        SRR13675771_2
        96.9%
        52%
        0.1
        SRR13675772_1
        92.4%
        54%
        0.1
        SRR13675772_2
        92.1%
        54%
        0.1
        SRR13675773_1
        91.6%
        52%
        0.1
        SRR13675773_2
        90.8%
        51%
        0.1
        SRR13675774_1
        91.3%
        53%
        0.1
        SRR13675774_2
        91.9%
        52%
        0.1
        SRR13675775_1
        97.9%
        53%
        0.1
        SRR13675775_2
        97.7%
        53%
        0.1
        SRR13675776_1
        95.1%
        55%
        0.2
        SRR13675776_2
        92.8%
        54%
        0.2
        SRR13675777_1
        24.7%
        55%
        0.0
        SRR13675777_2
        14.7%
        53%
        0.0
        SRR13675778_1
        94.9%
        53%
        0.1
        SRR13675778_2
        94.6%
        53%
        0.1
        SRR13675779_1
        93.7%
        51%
        0.1
        SRR13675779_2
        91.9%
        50%
        0.1
        SRR13675780_1
        97.8%
        54%
        0.1
        SRR13675780_2
        97.3%
        53%
        0.1
        SRR13675781_1
        93.4%
        54%
        0.1
        SRR13675781_2
        92.1%
        55%
        0.1
        SRR13675782_1
        92.6%
        52%
        0.1
        SRR13675782_2
        91.8%
        51%
        0.1
        SRR13675783_1
        92.7%
        52%
        0.1
        SRR13675783_2
        92.6%
        51%
        0.1
        SRR13675784_1
        94.7%
        55%
        0.1
        SRR13675784_2
        93.6%
        54%
        0.1
        SRR13675785_1
        94.2%
        55%
        0.1
        SRR13675785_2
        92.6%
        54%
        0.1
        SRR13675786_1
        91.7%
        53%
        0.1
        SRR13675786_2
        90.4%
        52%
        0.1
        SRR13675787_1
        91.8%
        54%
        0.1
        SRR13675787_2
        90.6%
        53%
        0.1
        SRR13675788_1
        95.6%
        53%
        0.1
        SRR13675788_2
        94.5%
        52%
        0.1
        SRR13675789_1
        92.4%
        53%
        0.1
        SRR13675789_2
        91.7%
        52%
        0.1
        SRR13675790_1
        92.9%
        54%
        0.1
        SRR13675790_2
        91.6%
        53%
        0.1
        SRR13675791_1
        93.0%
        52%
        0.1
        SRR13675791_2
        92.1%
        52%
        0.1
        SRR13675792_1
        33.1%
        54%
        0.0
        SRR13675792_2
        25.3%
        52%
        0.0
        SRR13675793_1
        95.0%
        52%
        0.0
        SRR13675793_2
        94.0%
        51%
        0.0
        SRR13675794_1
        92.9%
        54%
        0.1
        SRR13675794_2
        91.5%
        53%
        0.1
        SRR13675795_1
        93.4%
        55%
        0.1
        SRR13675795_2
        91.9%
        54%
        0.1
        SRR13675796_1
        93.1%
        52%
        0.1
        SRR13675796_2
        91.7%
        52%
        0.1
        SRR13675797_1
        94.2%
        54%
        0.1
        SRR13675797_2
        92.9%
        53%
        0.1
        SRR13675798_1
        96.4%
        52%
        0.1
        SRR13675798_2
        95.4%
        51%
        0.1
        SRR13675799_1
        92.8%
        53%
        0.1
        SRR13675799_2
        91.9%
        52%
        0.1
        SRR13675800_1
        92.5%
        53%
        0.1
        SRR13675800_2
        91.2%
        52%
        0.1
        SRR13675801_1
        91.6%
        53%
        0.1
        SRR13675801_2
        91.7%
        53%
        0.1
        SRR13675802_1
        91.5%
        53%
        0.1
        SRR13675802_2
        91.1%
        53%
        0.1
        SRR13675803_1
        96.6%
        55%
        0.0
        SRR13675803_2
        95.9%
        54%
        0.0
        SRR13675804_1
        89.9%
        54%
        0.0
        SRR13675804_2
        87.6%
        54%
        0.0
        SRR13675805_1
        94.4%
        53%
        0.3
        SRR13675805_2
        91.4%
        52%
        0.3
        SRR13675806_1
        91.6%
        53%
        0.1
        SRR13675806_2
        89.8%
        52%
        0.1
        SRR13675807_1
        91.1%
        53%
        0.1
        SRR13675807_2
        89.9%
        53%
        0.1
        SRR13675808_1
        92.5%
        53%
        0.1
        SRR13675808_2
        92.0%
        51%
        0.1
        SRR13675809_1
        92.7%
        54%
        0.1
        SRR13675809_2
        92.3%
        53%
        0.1
        SRR13675810_1
        92.9%
        55%
        0.1
        SRR13675810_2
        92.3%
        55%
        0.1
        SRR13675811_1
        92.5%
        52%
        0.1
        SRR13675811_2
        90.2%
        51%
        0.1
        SRR13675812_1
        89.8%
        54%
        0.1
        SRR13675812_2
        89.7%
        53%
        0.1
        SRR13675813_1
        85.1%
        52%
        0.1
        SRR13675813_2
        87.2%
        52%
        0.1
        SRR13675814_1
        87.8%
        52%
        0.2
        SRR13675814_2
        89.1%
        53%
        0.2
        SRR13675815_1
        92.3%
        53%
        0.1
        SRR13675815_2
        92.1%
        53%
        0.1
        SRR13675816_1
        91.0%
        53%
        0.1
        SRR13675816_2
        90.8%
        55%
        0.1
        SRR13675817_1
        86.4%
        51%
        0.1
        SRR13675817_2
        88.9%
        51%
        0.1
        SRR13675818_1
        88.6%
        51%
        0.2
        SRR13675818_2
        89.8%
        51%
        0.2
        SRR13675819_1
        91.9%
        52%
        0.1
        SRR13675819_2
        90.8%
        52%
        0.1
        SRR13675820_1
        92.7%
        53%
        0.2
        SRR13675820_2
        92.6%
        55%
        0.2
        SRR13675821_1
        91.3%
        53%
        0.1
        SRR13675821_2
        90.9%
        54%
        0.1
        SRR13675822_1
        89.4%
        50%
        0.2
        SRR13675822_2
        90.8%
        51%
        0.2
        SRR13675823_1
        83.6%
        51%
        0.1
        SRR13675823_2
        82.2%
        52%
        0.1
        SRR13675824_1
        94.3%
        52%
        0.1
        SRR13675824_2
        93.9%
        53%
        0.1
        SRR13675825_1
        86.7%
        54%
        0.0
        SRR13675825_2
        87.1%
        55%
        0.0
        SRR13675826_1
        89.6%
        51%
        0.3
        SRR13675826_2
        90.0%
        51%
        0.3
        SRR13675827_1
        88.1%
        51%
        0.2
        SRR13675827_2
        88.7%
        51%
        0.2
        SRR13675828_1
        92.0%
        53%
        0.2
        SRR13675828_2
        92.4%
        54%
        0.2
        SRR13675829_1
        90.4%
        53%
        0.1
        SRR13675829_2
        90.6%
        54%
        0.1
        SRR13675830_1
        91.5%
        54%
        0.1
        SRR13675830_2
        91.3%
        54%
        0.1
        SRR13675831_1
        89.3%
        52%
        0.2
        SRR13675831_2
        89.9%
        51%
        0.2
        SRR13675832_1
        88.4%
        52%
        0.2
        SRR13675832_2
        88.3%
        51%
        0.2
        SRR13675833_1
        93.4%
        52%
        0.2
        SRR13675833_2
        93.3%
        53%
        0.2
        SRR13675834_1
        91.5%
        53%
        0.2
        SRR13675834_2
        91.4%
        52%
        0.2
        SRR13675835_1
        89.8%
        52%
        0.3
        SRR13675835_2
        90.4%
        51%
        0.3
        SRR13675836_1
        90.1%
        52%
        0.3
        SRR13675836_2
        90.1%
        51%
        0.3
        SRR13675837_1
        90.2%
        53%
        0.2
        SRR13675837_2
        90.9%
        54%
        0.2
        SRR13675838_1
        89.6%
        53%
        0.2
        SRR13675838_2
        90.8%
        52%
        0.2
        SRR13675839_1
        88.1%
        52%
        0.3
        SRR13675839_2
        88.4%
        51%
        0.3
        SRR13675840_1
        88.4%
        52%
        0.2
        SRR13675840_2
        89.6%
        53%
        0.2
        SRR13675841_1
        93.1%
        54%
        0.1
        SRR13675841_2
        92.8%
        53%
        0.1
        SRR13675842_1
        94.8%
        52%
        0.1
        SRR13675842_2
        94.5%
        53%
        0.1
        SRR13675843_1
        92.9%
        56%
        0.4
        SRR13675843_2
        91.8%
        56%
        0.4
        SRR13675844_1
        87.7%
        52%
        0.2
        SRR13675844_2
        89.3%
        52%
        0.2
        SRR13675845_1
        88.3%
        52%
        0.2
        SRR13675845_2
        89.0%
        52%
        0.2
        SRR13675846_1
        91.0%
        54%
        0.1
        SRR13675846_2
        90.6%
        55%
        0.1
        SRR13675847_1
        92.3%
        56%
        0.2
        SRR13675847_2
        90.6%
        56%
        0.2
        SRR13675848_1
        88.7%
        52%
        0.2
        SRR13675848_2
        89.6%
        51%
        0.2
        SRR13675849_1
        89.1%
        51%
        0.2
        SRR13675849_2
        89.2%
        51%
        0.2
        SRR13675850_1
        94.2%
        53%
        0.1
        SRR13675850_2
        93.6%
        54%
        0.1
        SRR13675851_1
        89.5%
        56%
        0.1
        SRR13675851_2
        88.2%
        55%
        0.1
        SRR13675852_1
        91.7%
        53%
        0.1
        SRR13675852_2
        91.6%
        53%
        0.1
        SRR13675853_1
        90.3%
        52%
        0.3
        SRR13675853_2
        89.9%
        51%
        0.3
        SRR13675854_1
        89.1%
        53%
        0.2
        SRR13675854_2
        89.8%
        52%
        0.2
        SRR13675855_1
        89.5%
        54%
        0.2
        SRR13675855_2
        91.3%
        54%
        0.2
        SRR13675856_1
        89.4%
        56%
        0.1
        SRR13675856_2
        88.2%
        56%
        0.1
        SRR13675857_1
        88.6%
        52%
        0.2
        SRR13675857_2
        89.2%
        52%
        0.2
        SRR13675858_1
        88.4%
        52%
        0.2
        SRR13675858_2
        88.9%
        52%
        0.2
        SRR13675859_1
        93.4%
        53%
        0.2
        SRR13675859_2
        93.3%
        54%
        0.2
        SRR13675860_1
        89.9%
        55%
        0.2
        SRR13675860_2
        89.7%
        55%
        0.2
        SRR13675861_1
        89.6%
        51%
        0.2
        SRR13675861_2
        91.3%
        51%
        0.2
        SRR13675862_1
        90.5%
        53%
        0.1
        SRR13675862_2
        90.7%
        54%
        0.1
        SRR13675863_1
        91.7%
        52%
        0.1
        SRR13675863_2
        90.7%
        52%
        0.1
        SRR13675864_1
        94.0%
        53%
        0.2
        SRR13675864_2
        93.3%
        54%
        0.2
        SRR13675865_1
        89.5%
        54%
        0.1
        SRR13675865_2
        88.9%
        54%
        0.1
        SRR13675866_1
        88.1%
        52%
        0.2
        SRR13675866_2
        88.7%
        52%
        0.2
        SRR13675867_1
        89.1%
        53%
        0.2
        SRR13675867_2
        89.1%
        53%
        0.2
        SRR13675868_1
        92.1%
        53%
        0.1
        SRR13675868_2
        92.4%
        54%
        0.1
        SRR13675869_1
        90.1%
        55%
        0.2
        SRR13675869_2
        89.5%
        55%
        0.2
        SRR13675870_1
        87.2%
        53%
        0.2
        SRR13675870_2
        88.3%
        52%
        0.2
        SRR13675871_1
        88.0%
        52%
        0.2
        SRR13675871_2
        89.0%
        53%
        0.2
        SRR13675872_1
        91.8%
        54%
        0.2
        SRR13675872_2
        91.5%
        55%
        0.2
        SRR13675873_1
        89.2%
        54%
        0.2
        SRR13675873_2
        89.3%
        54%
        0.2
        SRR13675874_1
        92.7%
        51%
        0.1
        SRR13675874_2
        89.4%
        52%
        0.1
        SRR13675875_1
        89.6%
        52%
        0.2
        SRR13675875_2
        90.4%
        51%
        0.2
        SRR13675876_1
        89.1%
        53%
        0.2
        SRR13675876_2
        88.8%
        51%
        0.2
        SRR13675877_1
        91.5%
        54%
        0.1
        SRR13675877_2
        90.5%
        55%
        0.1
        SRR13675878_1
        90.4%
        53%
        0.2
        SRR13675878_2
        90.0%
        54%
        0.2
        SRR13675879_1
        89.2%
        52%
        0.2
        SRR13675879_2
        88.7%
        52%
        0.2
        SRR13675880_1
        89.0%
        52%
        0.2
        SRR13675880_2
        88.4%
        52%
        0.2
        SRR13675881_1
        90.0%
        51%
        0.2
        SRR13675881_2
        90.9%
        51%
        0.2
        SRR13675882_1
        95.7%
        50%
        0.2
        SRR13675882_2
        93.6%
        51%
        0.2
        SRR13675883_1
        93.3%
        52%
        0.1
        SRR13675883_2
        93.5%
        53%
        0.1
        SRR13675884_1
        95.7%
        52%
        0.2
        SRR13675884_2
        93.2%
        53%
        0.2
        SRR13675885_1
        92.9%
        54%
        0.1
        SRR13675885_2
        92.5%
        53%
        0.1
        SRR13675886_1
        95.4%
        52%
        0.2
        SRR13675886_2
        92.7%
        52%
        0.2
        SRR13675887_1
        97.7%
        52%
        0.1
        SRR13675887_2
        96.6%
        53%
        0.1
        SRR13675888_1
        96.2%
        55%
        0.1
        SRR13675888_2
        93.6%
        55%
        0.1
        SRR13675889_1
        94.8%
        51%
        0.1
        SRR13675889_2
        92.7%
        51%
        0.1
        SRR13675890_1
        95.1%
        51%
        0.2
        SRR13675890_2
        93.2%
        51%
        0.2
        SRR13675891_1
        97.1%
        54%
        0.2
        SRR13675891_2
        95.8%
        54%
        0.2
        SRR13675892_1
        95.9%
        54%
        0.1
        SRR13675892_2
        92.7%
        53%
        0.1
        SRR13675893_1
        96.1%
        53%
        0.2
        SRR13675893_2
        93.9%
        53%
        0.2
        SRR13675894_1
        96.4%
        53%
        0.1
        SRR13675894_2
        94.1%
        55%
        0.1
        SRR13675895_1
        96.0%
        52%
        0.1
        SRR13675895_2
        93.7%
        52%
        0.1
        SRR13675896_1
        91.6%
        54%
        0.1
        SRR13675896_2
        90.5%
        54%
        0.1
        SRR13675897_1
        95.0%
        53%
        0.1
        SRR13675897_2
        86.5%
        54%
        0.1
        SRR13675898_1
        95.6%
        52%
        0.2
        SRR13675898_2
        92.6%
        51%
        0.2
        SRR13675899_1
        95.5%
        51%
        0.2
        SRR13675899_2
        92.3%
        50%
        0.2
        SRR13675900_1
        97.6%
        57%
        0.1
        SRR13675900_2
        95.6%
        56%
        0.1
        SRR13675901_1
        97.2%
        53%
        0.1
        SRR13675901_2
        95.9%
        54%
        0.1
        SRR13675902_1
        95.5%
        50%
        0.1
        SRR13675902_2
        93.7%
        49%
        0.1
        SRR13675903_1
        97.1%
        53%
        0.2
        SRR13675903_2
        94.7%
        52%
        0.2
        SRR13675904_1
        95.2%
        52%
        0.2
        SRR13675904_2
        92.8%
        51%
        0.2
        SRR13675905_1
        95.6%
        54%
        0.1
        SRR13675905_2
        92.0%
        55%
        0.1
        SRR13675906_1
        95.5%
        51%
        0.2
        SRR13675906_2
        92.5%
        52%
        0.2
        SRR13675907_1
        91.5%
        52%
        0.1
        SRR13675907_2
        90.5%
        52%
        0.1
        SRR13675908_1
        92.8%
        54%
        0.1
        SRR13675908_2
        91.4%
        53%
        0.1
        SRR13675909_1
        90.1%
        53%
        0.1
        SRR13675909_2
        89.4%
        53%
        0.1
        SRR13675910_1
        94.5%
        51%
        0.1
        SRR13675910_2
        91.1%
        52%
        0.1
        SRR13675911_1
        96.5%
        53%
        0.1
        SRR13675911_2
        94.4%
        54%
        0.1
        SRR13675912_1
        96.3%
        53%
        0.1
        SRR13675912_2
        93.2%
        54%
        0.1
        SRR13675913_1
        95.6%
        52%
        0.2
        SRR13675913_2
        92.8%
        52%
        0.2
        SRR13675914_1
        96.8%
        53%
        0.2
        SRR13675914_2
        94.2%
        54%
        0.2
        SRR13675915_1
        95.8%
        53%
        0.1
        SRR13675915_2
        93.2%
        54%
        0.1
        SRR13675916_1
        95.1%
        50%
        0.1
        SRR13675916_2
        92.6%
        51%
        0.1
        SRR13675917_1
        95.0%
        50%
        0.1
        SRR13675917_2
        92.3%
        51%
        0.1
        SRR13675918_1
        96.9%
        53%
        0.1
        SRR13675918_2
        95.2%
        54%
        0.1
        SRR13675919_1
        95.2%
        53%
        0.1
        SRR13675919_2
        91.9%
        54%
        0.1
        SRR13675920_1
        91.2%
        53%
        0.1
        SRR13675920_2
        90.2%
        52%
        0.1
        SRR13675921_1
        95.1%
        51%
        0.1
        SRR13675921_2
        92.4%
        50%
        0.1
        SRR13675922_1
        95.4%
        52%
        0.1
        SRR13675922_2
        92.4%
        51%
        0.1
        SRR13675923_1
        97.6%
        52%
        0.1
        SRR13675923_2
        96.8%
        52%
        0.1
        SRR13675924_1
        95.9%
        55%
        0.1
        SRR13675924_2
        92.3%
        55%
        0.1
        SRR13675925_1
        95.0%
        51%
        0.1
        SRR13675925_2
        92.1%
        50%
        0.1
        SRR13675926_1
        95.4%
        51%
        0.1
        SRR13675926_2
        92.0%
        50%
        0.1
        SRR13675927_1
        97.5%
        53%
        0.1
        SRR13675927_2
        96.2%
        54%
        0.1
        SRR13675928_1
        95.1%
        53%
        0.1
        SRR13675928_2
        92.5%
        54%
        0.1
        SRR13675929_1
        95.0%
        51%
        0.2
        SRR13675929_2
        92.6%
        51%
        0.2
        SRR13675930_1
        95.2%
        51%
        0.2
        SRR13675930_2
        92.2%
        52%
        0.2
        SRR13675931_1
        95.6%
        53%
        0.1
        SRR13675931_2
        95.4%
        51%
        0.1
        SRR13675932_1
        97.1%
        52%
        0.1
        SRR13675932_2
        96.2%
        52%
        0.1
        SRR13675933_1
        93.0%
        53%
        0.1
        SRR13675933_2
        89.9%
        53%
        0.1
        SRR13675934_1
        95.6%
        51%
        0.2
        SRR13675934_2
        92.5%
        51%
        0.2
        SRR13675935_1
        95.8%
        52%
        0.2
        SRR13675935_2
        92.5%
        52%
        0.2
        SRR13675936_1
        97.4%
        52%
        0.1
        SRR13675936_2
        95.6%
        51%
        0.1
        SRR13675937_1
        92.8%
        52%
        0.0
        SRR13675937_2
        89.7%
        53%
        0.0
        SRR13675938_1
        95.2%
        50%
        0.2
        SRR13675938_2
        92.4%
        51%
        0.2
        SRR13675939_1
        94.7%
        51%
        0.1
        SRR13675939_2
        91.9%
        51%
        0.1
        SRR13675940_1
        94.7%
        52%
        0.0
        SRR13675940_2
        93.1%
        52%
        0.0
        SRR13675941_1
        95.5%
        52%
        0.2
        SRR13675941_2
        92.8%
        51%
        0.2
        SRR13675942_1
        91.5%
        53%
        0.1
        SRR13675942_2
        91.7%
        51%
        0.1
        SRR13675943_1
        97.1%
        53%
        0.2
        SRR13675943_2
        94.8%
        52%
        0.2
        SRR13675944_1
        94.2%
        52%
        0.0
        SRR13675944_2
        91.7%
        53%
        0.0
        SRR13675945_1
        95.5%
        52%
        0.2
        SRR13675945_2
        92.2%
        51%
        0.2
        SRR13675946_1
        94.6%
        52%
        0.1
        SRR13675946_2
        91.2%
        52%
        0.1

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (300bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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